A recent epidemiological study showed that daily intake of mg quantities of S-equol is required for health-promoting effects in menopausal women. However, the maximum equol content in food was reported to be approximately 130 μg/100 g in egg yolk. The objective of this study was to find a high equol-containing food. We measured the equol content of 33 egg yolks and 21 fermented soybean foods. Equol was detected in 28 egg yolks at the maximum content of 43 μg/100 g. In the fermented soybean foods, equol was detected only in stinky tofu. We examined 16 stinky tofu samples purchased during different seasons and the average equol content was 1.39 mg/100 g, ranging from 0.34 to 2.68 mg/100 g. Equol was present in stinky tofu as the S-enantiomeric form and as an aglycon type. This is the first report demonstrating that stinky tofu contains high levels of S-equol, which may exert beneficial effects in menopausal women.